The Newton-Raphson step in the Block Update Operator now throws an Operator Failed Exception rather than a runtime exception when it does not coverge in the specified number of steps. This allows BEAST to continue running even if the block-updater doesn't work occasionally.
47 lines of code changed in 1 file:
Added a tracer class that does importance sampling for the gmrf fixed grid.
104 lines of code changed in 1 file:
Fixed <leafTrait> element in TreeModel. Used for extracting a single trait parameter for a leaf.
3 lines of code changed in 1 file:
Fixed <leafTrait> element in TreeModel. Used for extracting a single trait parameter for a leaf.
419 lines of code changed in 2 files:
remove duplicate replaceParameter
48 lines of code changed in 1 file:
Another improvement in efficency.
67 lines of code changed in 1 file:
Improved the efficiency of CompatibilityStatistic enormously by using BitSets. Still very slow for large trees. This is because it does a full traversal of the tree for each test and for each nodes compares against the set of clades in the constraints tree (breaks out as soon as an incompatibility is found).
88 lines of code changed in 2 files:
Just some minor fixes to the Fixed Grid logger. Checked on an example, checks out ok.
1 lines of code changed in 1 file:
Fixed a bug introduced into FlexibleNode.insertChild in a recent update (use of System.arrayCopy).
Also fixed another parser discrepancy in TreeModelParser.
1004 lines of code changed in 4 files:
Fixed a few bugs in the birth-death XML generation.
15 lines of code changed in 2 files:
Added some extra features to the fixed grid logger.
56 lines of code changed in 1 file:
Move getParameter and replaceParameter to AbstractXMLObjectParser - now used by multiple parsers
Renamed getSocketChild
Added generic 'public <T> T getAttribute(String name, T defaultValue)' to XMLObject - some usages of getXXXXattribute replaced. Update usage in your code if possible so we can one day remove the numerous getXXXXattribute
364 lines of code changed in 76 files:
cleanup: remove spurios old comments
4 lines of code changed in 1 file:
Some improvements for mixing with relaxed clock models
452 lines of code changed in 6 files:
Added a flag to TreeLikelihood to allow missing taxa (defaults to false so that missing taxa throw an exception). If true then missing taxa are given missing data at all sites.
455 lines of code changed in 7 files:
Added the GMRFSkyrideFixedGridLogger that projects the skyride random grid onto a fixed grid. Had to add an extra method to GMRFSkyrideLikelihood too.
220 lines of code changed in 3 files:
Small fix to this: Added a tree compatibility statistic. This takes the current tree and a (presumably) less resolved tree and tests whether they are compatible. This allows us to test compatibility with a 'constraints' tree rather than doing lots of monophyly constraints.
10 lines of code changed in 1 file:
Added a tree compatibility statistic. This takes the current tree and a (presumably) less resolved tree and tests whether they are compatible. This allows us to test compatibility with a 'constraints' tree rather than doing lots of monophyly constraints.
205 lines of code changed in 3 files:
Made a small mistake in my last commit: Fixed a couple of parser definitions that were giving warnings of unrecognized elements (thanks, Joseph, for putting this checking in).
1 lines of code changed in 1 file:
Fixed a couple of parser definitions that were giving warnings of unrecognized elements (thanks, Joseph, for putting this checking in).
47 lines of code changed in 3 files:
Added option in ScaleOperator to update all dimensions independently and simultaneously. Takes care of a severe mixing problem Philippe is having with the discrete diffusion model. For geographies with > 10 or so locations, we need to consider rjMCMC to add/remove rates instead of SSVS.
444 lines of code changed in 3 files:
Fix to do lazy sampling of ancestral states.
15 lines of code changed in 1 file:
Fixed sync problem in AncestralState. Must be called getNodeCount # of times.
5 lines of code changed in 1 file:
Checking out the use of the diffusion model for univariate processes. Added testComparativeMethod.xml to this aim. There's a broken bit in the TreeModelParser -- does find leafTaxon traits like it used to. ????
542 lines of code changed in 4 files:
Updated Build number in BeastVersion
3 lines of code changed in 2 files:
silly typo
1 lines of code changed in 1 file:
Do not parse local elements declares by XML rules with global parsers.
Add checks for incorrect XML files. Issue warnings, but running with -strict makes them errors. Report unexpected elements, i.e. unused elements.
169 lines of code changed in 14 files:
code cleanup
22 lines of code changed in 1 file:
small cleanup
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import optimize
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comment
5 lines of code changed in 1 file:
correct one possible bug from a warning, fix other warnings
15 lines of code changed in 1 file:
Fixed various sources of NEXUS tree files so that they automatically enclose taxon labels in quotes if they contain spaces or other problematic characters.
30 lines of code changed in 3 files:
add option to condition analysis on number of changes
24 lines of code changed in 2 files:
call finalize() of parent class
4 lines of code changed in 1 file:
comment out unused code
2 lines of code changed in 1 file:
add missing exception signature
1 lines of code changed in 1 file:
TN93 (Tamura and Nei) substitution model
471 lines of code changed in 2 files:
Added a logger that logs an ancestral state reconstruction for a given MRCA.
138 lines of code changed in 2 files:
Add output of coalecent bins
196 lines of code changed in 7 files:
fix another case of a never reached print statment
18 lines of code changed in 1 file:
readability
9 lines of code changed in 1 file:
Fixed the parser for differenceStatistic
13 lines of code changed in 2 files:
import of deleted file
0 lines of code changed in 1 file:
8 lines of code changed in 1 file:
updated yule tests. Removed old birth death models
312 lines of code changed in 6 files:
small cleanup
4 lines of code changed in 1 file:
small cleanup
1 lines of code changed in 1 file:
remove unused code
15 lines of code changed in 1 file:
use midpoints option
38 lines of code changed in 3 files:
birth death model
261 lines of code changed in 6 files:
rename of class
348 lines of code changed in 2 files:
updated to log trees in nexus
6 lines of code changed in 1 file:
interface comments
20 lines of code changed in 1 file:
code cleanup
43 lines of code changed in 2 files:
java 5 loops
5 lines of code changed in 1 file:
Call non-node specific function first, to allow it to do per-taxa preprocessing if required
3 lines of code changed in 1 file:
code police (make variable local)
2 lines of code changed in 1 file:
Comment out unused statments
3 lines of code changed in 1 file:
spelling and stuff
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Some early code of Marc's before he knew what he was doing ;-) removed with his blessing.
0 lines of code changed in 1 file:
MIssing attribute specification
2 lines of code changed in 1 file:
Simple expression statistic (RPN based)
272 lines of code changed in 3 files:
toString() now calls getLogLikelihood to properly evalute the likelihood (previously only return the value of 'logLikelihood' which may not have been calculated). This will probably only be called when a treeLikelihood is put in a <report> element in the XML as it is used in testLikelihood.xml to check treeLikelihood give similar values to PAUP.
1 lines of code changed in 1 file:
New birth death model conditioned on # taxa
122 lines of code changed in 2 files:
Fixed bug in TreeAnnotator where it was writing all posterior probabilities as zero.
9 lines of code changed in 1 file:
[FIX] Enable compilation using 'ant'
* build.xml: update lib/* elements
* build_release.xml: ditto.
8 lines of code changed in 2 files:
Did not mean to commit latest changes to RandomWalkOnMapOperator because they depend on many other changes that I have not yet debugged.
13 lines of code changed in 1 file: